A historical and critical analysis of the concept of the gene that attempts to provide new perspectives and metaphors for the transformation of biology and its philosophy.

Abstract: Many believe that, in addition to cognitive capacities, autonomous robots need something similar to affect. As in humans, affect, including specific emotions, would filter robot experience based on a set of goals, values, and interests. This narrows behavioral options and avoids combinatorial explosion or regress problems that challenge purely cognitive assessments in a continuously changing experiential field. Adding human-like affect to robots is not straightforward, however. Affect in organisms is an aspect of evolved biological systems, from the taxes of (...) single-cell organisms to the instincts, drives, feelings, moods, and emotions that focus human behavior through the mediation of hormones, pheromones, neurotransmitters, the autonomic nervous system, and key brain structures. We argue that human intelligence is intimately linked to biological affective systems and to the unique repertoire of potential behaviors, sometimes conflicting, they facilitate. Artificial affect is affect in name only and without genes and biological bodies, autonomous robots will lack the goals, interests, and value systems associated with human intelligence. We will take advantage of their general intelligence and expertise, but robots will not enter our intellectual world or apply for legal status in the community. -/- . (shrink)

The concept of the gene has been the central organizing theme of 20th century biology. Biology has become increasingly influential both for philosophers seeking a naturalized basis for epistemology, ethics, and the understanding of the mind, as well as for the human sciences generally. The central task of this work is to get the story right about genes and in so doing provide a critical and enabling resourse for use in the further pursuit of human self-understanding. ;The work begins (...) with a wide-ranging historical reconstruction and conceptual analysis of the meaning of "the gene" that results in defining and distinguishing two different "genes". Each of these can be seen as an heir to one of the two major historical trends in explaining the source of biological order---preformationism and epigenesis. The preformationist gene predicts phenotypes but only on an instrumental basis where immediate medical and/or economic benefits can be had. The gene of epigenesis , by contrast, is a developmental resource that provides templates for RNA and protein synthesis but has in itself no determinate relationship to organismal phenotypes. The seemingly prevalent idea that genes constitute information for traits is based, I argue, upon an unwarranted conflation of these two senses which is in effect held together by rhetorical glue. Beyond this historical, conceptual, and rhetorical inquiry the bulk of the dissertation then concerns itself with an empirically up-to-date analysis of the cell and molecular basis of biological order and of the pathological loss of same. In each of these chapters I structure my analysis with the idea in mind that the "conflated" view can be held empirically accountable. Major touchpoints in this work include the ideas of I. Kant, J. Blumenbach, K. E. von Baer, J. Muller, R. Virchow, W. Johannsen, R. Falk, J. Sapp, E. Schrodinger, M. Delbruick, G. Gamow, R. Doyle, L. Kay, S. Kauffman, E. Jablonka, J. Rothman, K. Yamamoto, P. Rous, H. Temin, J. M. Bishop, H. Harris, E. Stanbridge, D. L. Smithers, B. Vogelstein, E. Farber and H. Rubin. (shrink)

If the question ``What is a gene?'' proves to be worth asking it must be able to elicit an answer which both recognizes and address the reasons why the concept of the gene ever seemed to be something worth getting excited about in the first place as well analyzing and evaluating the latest develops in the molecular biology of DNA. Each of the preceding papers fails to do one of these and sufferrs the consequences. Where Rolston responds to (...) the apparent failure of molecular biology to make good on the desideratum of the classical gene by veering off into fanciful talk about ``cybernetic genes,'' Griffiths and Stotz lose themselves in the molecular fine print and forget to ask themselves why ``genes'' should be of any special interst anyway. (shrink)

In her recent book Lindley Darden has endeavored to reclaim for philosophy an active role in the elaboration of good science. She has done this, not by holding up some set of rational standards derived from outside of scientific practice, but rather by delving into the history of science and coming out with a set of scientific strategies. Unconcerned about whether any particular strategy wasin fact employed in a given historical case her project depends upon two claims, first that these (...) strategiescould have been successfully deployed in the particular cases from which they were construed, and second and more importantly, that these strategies can be generalized beyond any particular context and be put to future use. It will be argued that Darden''s conception of the possible context independence of scientific strategies is based upon an overly cognitivist misconstrual. An alternative account of the relationship of context dependent and context independent aspects of scientific theory formation will be offered as well as its implications for philosophy. (shrink)

The essays in this book discuss human behavior and the institutions of capitalism. The essays are non-technical and are written so as to be accessible to students of all disciplines and to all other persons interested in capitalism and in economic behavior. They often present unconventional views of the topics they discuss. Those containing unconventional views discuss self-interested behavior, selfish gene theory, the meaning and social function of private ownership, the externality problem, the nature of the firm and the (...) rise of capitalism. The essays are not meant to be a textbook, but they offer a useful supplementary reading source for courses in business, economics and law that deal with human behavior in the marketplace and with capitalism, ownership, markets and firms. (shrink)

Radically new or unexpected findings in a science demand an openness to new concepts and styles of explanation. The time is more than ripe for asking ourselves what we have learned from the research program of comparative genomics. Where not long ago the human genome was expected to reveal a close association of complexity with the quantitative expansion of the roster of unique genes, more recent findings, especially in relation to comparisons between human and chimp, have raised the bracing possibility (...) that when it comes to complexity, it may be that `less is more'. But `less is more' is not the only observation or inference that follows from the data. The idea of `progressive detachment' will be introduced and set forth as the most perspicuous conceptual resource for unifying and interpreting the overall findings from comparative genomics to date. (shrink)

Vaccinia virus, the world's oldest vaccine, was used originally for the eradication of smallpox. It is now being genetically engineered to create new live vaccines for use against other infectious agents of medical and veterinary importance. Genes coding for antigens of several pathogens have been linked to vaccinia virus transcriptional regulatory signals and inserted into the vaccinia virus genome. The resultant recombinant viruses are infectious, express the foreign gene, stimulate specific immune responses in vaccinated animals and can protect against (...) disease caused by the corresponding pathogen. (shrink)

Recognition of the plasticity of development — from gene expression to neuroplasticity — is increasingly undermining the traditional distinction between structure and function, or anatomy and behavior. At the same time, dynamic systems theory — a set of tools and concepts drawn from the physical sciences — has emerged as a way of describing what Maurice Merleau-Ponty calls the “dynamic anatomy” of the living organism. This article surveys and synthesizes dynamic systems models of development from biology, neuroscience, and psychology (...) in order to propose an integrated account of growth, learning, and behavior. Key to this account is the concept of self-differentiation or symmetry-breaking. I argue that development can be understood as a cascade of symmetry-breaking events brought about by the ongoing interactions of multiple, nested, nonlinear dynamic systems whose self-organizing behaviors gradually alter their own anatomical conditions. I begin by introducing the concept of symmetry-breaking as a way of understanding anatomical development. I then extend this approach to motor development by arguing that the organism’s behavior grows along with its body, like a new organ. Finally, I argue that the organism’s behavior and its world grow together dialectically, each driving the other to become more complex and asymmetrical through its own increasing asymmetry. Thus development turns out to be a form of cognition or sense-making, and cognition a form of development. (shrink)

Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because (...) proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at http://pir.georgetown.edu/pro/. (shrink)

The Protein Ontology (PRO) is designed as a formal and principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from a classification of proteins on the basis of evolutionary relationships at the homeomorphic level to the representation of the multiple protein forms of a gene, including those resulting from alternative splicing, cleavage and/or posttranslational modifications. Focusing specifically on the TGF-beta signaling proteins, we describe the building, curation, usage and dissemination of PRO. PRO provides a (...) framework for the formal representation of protein classes and protein forms in the OBO Foundry. It is designed to enable data retrieval and integration and machine reasoning at the molecular level of proteins, thereby facilitating cross-species comparisons, pathway analysis, disease modeling and the generation of new hypotheses. (shrink)

The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO (...) relates to UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (shrink)

Book review of Lenny Moss, What Genes Can’t Do. Cambridge, MA: MIT Press , 256 pp. -/- Many philosophers of science will have encountered the core distinction between two different gene concepts found in What Genes Can’t Do. Moss argues that contemporary uses of the term ‘gene’ that denote an information bearing entity result from the conflation of two concepts (‘Gene-P’ and ‘Gene-D’).

Philosophy of Science, 73 (April 2006) pp. 247–257. 0031-8248/2006/7302-0007$10.00 Copyright 2006 by the Philosophy of Science Association. All rights reserved. 247 BOOK REVIEWS Lenny Moss, What Genes Can’t Do . Cambridge, MA: MIT Press (2004), 256 pp., $21.00 (paper). Many philosophers of science will have encountered the core distinction between two different gene concepts found in What Genes Can’t Do . Moss argues that contemporary uses of the term ‘gene’ that denote an infor- mation bearing entity (...) result from the conflation of two concepts (‘Gene- P’ and ‘Gene-D’). These concepts arise out of distinct trajectories in the history of biology (preformation and epigenesis, respectively) but are glued together by the rhetoric of linguistic and textual metaphors (e.g., blueprints and programs). Gene-P picks out an instrumentalist use of ‘gene’ as phenotypic indicator or predictor, whereas Gene-D refers to DNA sequences as developmental template resources for RNA and pro- tein products that play variegated cellular roles in the production of many, distinct phenotypes. A number of critical responses to the distinction are now extant in the literature, but my aim is to answer a different question. Why should philosophers of science who have not read the book be interested in it (besides the fact that it is now available in paperback)? The answer is found at the level of methodology and is relevant to crit- icisms of Moss’s distinction. (shrink)

This article examines how minimal genome research mobilizes philosophical concepts such as minimality and essentiality. Following a historical approach the article aims to uncover what function this terminology plays and which problems are raised by them. Specifically, four historical moments are examined, linked to the work of Harold J. Morowitz, Mitsuhiro Itaya, Eugene Koonin and Arcady Mushegian, and J. Craig Venter. What this survey shows is a historical shift away from historical questions about life or descriptive questions about specific (...) organisms towards questions that explore biological possibilities: what are possible forms of minimal genomes, regardless of whether they exist in nature? Moreover, it highlights a fundamental ambiguity at work in minimal genome research between a universality claim and a standardization claim: does a minimal genome refer to the minimal gene set for any organism whatsoever? Or does it refer rather to a gene set that will provide stable, robust and predictable behaviour, suited for biotechnological applications? Two diagnoses are proposed for this ambiguity: a philosophical diagnosis of how minimal genome research either misunderstands the ontology of biological entities or philosophically misarticulates scientific practice. Secondly, a historical diagnosis that suggests that this ambiguity is part of a broader shift towards technoscience. (shrink)

Book Review: What Genes Can’t Do By Lenny Moss .

In March 1996, the General Accounting Office (GAO) issued the reportScientific Research: Continued Vigilance Critical to Protecting Human Subjects.It stated that “an inherent conflict of interest exists when physician-researchers include their patients in research protocols. If the physicians do not clearly distinguish between research and treatment in their attempt to inform subjects, the possible benefits of a study can be overemphasized and the risks minimized.” The report also acknowledged that “the line between research and treatment is not always cleartoclinicians. Controversy (...) exists regarding whether certain medical procedures should be categorized as research.”This problem currently plagues gene transfer research. A few months prior to the GAO report, an ad hoc committee appointed by National Institutes of Health (NIH) Director Harold Varmus expressed similar concerns in its assessment of NIH investment in research on gene therapy. (shrink)

In March 1996, the General Accounting Office issued the report Scientific Research: Continued Vigilance Critical to Protecting Human Subjects. It stated that “an inherent conflict of interest exists when physician-researchers include their patients in research protocols. If the physicians do not clearly distinguish between research and treatment in their attempt to inform subjects, the possible benefits of a study can be overemphasized and the risks minimized.” The report also acknowledged that “the line between research and treatment is not always clear (...) to clinicians. Controversy exists regarding whether certain medical procedures should be categorized as research.”This problem currently plagues gene transfer research. A few months prior to the GAO report, an ad hoc committee appointed by National Institutes of Health Director Harold Varmus expressed similar concerns in its assessment of NIH investment in research on gene therapy. (shrink)

In March 1996, the General Accounting Office (GAO) issued the reportScientific Research: Continued Vigilance Critical to Protecting Human Subjects.It stated that “an inherent conflict of interest exists when physician-researchers include their patients in research protocols. If the physicians do not clearly distinguish between research and treatment in their attempt to inform subjects, the possible benefits of a study can be overemphasized and the risks minimized.” The report also acknowledged that “the line between research and treatment is not always cleartoclinicians. Controversy (...) exists regarding whether certain medical procedures should be categorized as research.”This problem currently plagues gene transfer research. A few months prior to the GAO report, an ad hoc committee appointed by National Institutes of Health (NIH) Director Harold Varmus expressed similar concerns in its assessment of NIH investment in research on gene therapy. (shrink)

Traditional procedures for rational updating fail when it comes to self-locating opinions, such as your credences about where you are and what time it is. This paper develops an updating procedure for rational agents with self-locating beliefs. In short, I argue that rational updating can be factored into two steps. The first step uses information you recall from your previous self to form a hypothetical credence distribution, and the second step changes this hypothetical distribution to reflect information you have genuinely (...) learned as time has passed. While the second step resembles traditional procedures of updating by conditionalization, the first is best understood by analogy to traditional models of how agents transmit self-locating opinions through ordinary interpersonal communication. (shrink)

Porphyry’s position in the ancient hermeneutic tradition should be considered separately from his place in the Platonic tradition. He shows considerable respect for allegorizing interpreters with links to Pythagoreanism, particularly Numenius and Cronius, prominent sources in On the Cave of the Nymphs. The language of Homer’s Cave passage is demonstrably distinctive, resembling the Shield passage in the Iliad, and such as to suggest an ecphrasis to early imperial readers. Ecphrasis in turn suggested deeper significance for the story. While largely content (...) to follow Numenian trends in interpreting Homer’s cave symbolically and in relation to multiple belief-systems, Porphyry shows occasionally signs of wanting to adhere more closely to Homeric evidence, resorting to symbolic interpretation mainly when no more straightforward truth is on offer. (shrink)

If there is any consensus about knowledge in contemporary epistemology, it is that there is one primary kind: knowledge-that. I put forth a view, one I find in the works of Aristotle, on which knowledge-of – construed in a fairly demanding sense, as being well-acquainted with things – is the primary, fundamental kind of knowledge. As to knowledge-that, it is not distinct from knowledge-of, let alone more fundamental, but instead a species of it. To know that such-and-such, just like to (...) know a person or place, is to be well-acquainted with a portion of reality – in this case a fact. In part by comparing classic Gettier cases to cases in which one has true impressions of but fails to know a person, I argue that this account not only respects our intuitions about knowledge-that – in particular that it is or entails non-accidentally true justified belief – but also explains them, providing a compelling analysis. (shrink)

In The Neoplatonic Socrates, leading scholars in classics and philosophy address this gap by examining Neoplatonic attitudes toward the Socratic method, Socratic love, Socrates's divine mission and moral example, and the much-debated issue of moral rectitude. Collectively, they demonstrate the importance of Socrates for the majority of Neoplatonists, a point that has often been questioned owing to the comparative neglect of surviving commentaries on the Alcibiades, Gorgias, Phaedo, and Phaedrus, in favor of dialogues dealing explicitly with metaphysical issues. Supplemented with (...) a contextualizing introduction and a substantial appendix detailing where evidence for Socrates can be found in the extant literature, The Neoplatonic Socrates makes a clear case for the significant place Socrates held in the education and philosophy of late antiquity. (shrink)

Today the name Socrates invokes a powerful idealization of wisdom and nobility that would surprise many of his contemporaries, who excoriated the philosopher for corrupting youth. The problem of who Socrates "really" was—the true history of his activities and beliefs—has long been thought insoluble, and most recent Socratic studies have instead focused on reconstructing his legacy and tracing his ideas through other philosophical traditions. But this scholarship has neglected to examine closely a period of philosophy that has much to reveal (...) about what Socrates stood for and how he taught: the Neoplatonic tradition of the first six centuries C.E., which at times decried or denied his importance yet relied on his methods. In The Neoplatonic Socrates, leading scholars in classics and philosophy address this gap by examining Neoplatonic attitudes toward the Socratic method, Socratic love, Socrates's divine mission and moral example, and the much-debated issue of moral rectitude. Collectively, they demonstrate the importance of Socrates for the majority of Neoplatonists, a point that has often been questioned owing to the comparative neglect of surviving commentaries on the Alcibiades, Gorgias, Phaedo, and Phaedrus, in favor of dialogues dealing explicitly with metaphysical issues. Supplemented with a contextualizing introduction and a substantial appendix detailing where evidence for Socrates can be found in the extant literature, The Neoplatonic Socrates makes a clear case for the significant place Socrates held in the education and philosophy of late antiquity. (shrink)

What is the self? And how does it relate to the body? In the second edition of Personal Identity, Harold Noonan presents the major historical theories of personal identity, particularly those of Locke, Leibniz, Butler, Reid and Hume. Noonan goes on to give a careful analysis of what the problem of personal identity is, and its place in the context of more general puzzles about identity. He then moves on to consider the main issues and arguments which are the (...) subject of current debate, including the work of Bernard Williams and Derek Parfit, and makes new and challenging interpretations of them. This new edition contains additional material assessing the biological approach which has become increasingly popular in recent years, and extends the treatment of indeterminate identity to take account of the epistemic view of vagueness. This book covers the problem of personal identity from its origin in Locke's work to the most recent debates in the philosophical literature, and will be invaluablereading for any student of the topic. (shrink)

Existing discussions of legal proof address a host of apparently disparate questions: What does it take to prove a fact beyond a reasonable doubt? Why is the reasonable doubt standard notoriously elusive, sometimes considered by courts to be impossible to define? Can the standard of proof by a preponderance of the evidence be defined in terms of probability thresholds? Why is statistical evidence often insufficient to meet the burden of proof? -/- This paper defends an account of proof that addresses (...) each of these questions. Where existing theories take a piecemeal approach to these puzzles, my theory develops an insight that unifies them—namely, the thesis that legal proof requires knowledge. Although this thesis may seem radical at first, I answer several common objections to it, and I argue that it does better than several competing accounts when it comes to making sense of our intuitions about what legal proof requires. (shrink)

This work has been selected by scholars as being culturally important and is part of the knowledge base of civilization as we know it. This work is in the public domain in the United States of America, and possibly other nations. Within the United States, you may freely copy and distribute this work, as no entity (individual or corporate) has a copyright on the body of the work. Scholars believe, and we concur, that this work is important enough to be (...) preserved, reproduced, and made generally available to the public. To ensure a quality reading experience, this work has been proofread and republished using a format that seamlessly blends the original graphical elements with text in an easy-to-read typeface. We appreciate your support of the preservation process, and thank you for being an important part of keeping this knowledge alive and relevant. (shrink)

This work is derived from the SERC "Logic for IT" Summer School Conference on Proof Theory held at Leeds University. The contributions come from acknowledged experts and comprise expository and research articles which form an invaluable introduction to proof theory aimed at both mathematicians and computer scientists.

While self-report data is a staple of modern psychological studies, they rely on participants accurately self-reporting. Two constructs that impede accurate results are insufficient effort responding and response styles. These constructs share conceptual underpinnings and both utilized to reduce cognitive effort when responding to self-report scales. Little research has extensively explored the relationship of the two constructs. The current study explored the relationship of the two constructs across even-point and odd-point scales, as well as before and after data cleaning procedures. (...) We utilized IRTrees, a statistical method for modeling response styles, to examine the relationship between IER and response styles. To capture the wide range of IER metrics available, we employed several forms of IER assessment in our analyses and generated IER factors based on the type of IER being detected. Our results indicated an overall modest relationship between IER and response styles, which varied depending on the type of IER metric being considered or type of scale being evaluated. As expected, data cleaning also changed the relationships of some of the variables. We posit the difference between the constructs may be the degree of cognitive effort participants are willing to expend. Future research and applications are discussed. (shrink)